You would have to try to make it happen on command so you can try to track it down.
If a fan suddenly has to speed up, maybe you hear it.
I once had a cpu fan slightly warped and hitting the heatsink. strange this is it would only happen sometimes. I do NOT think this is your cause since my fan was warped because my power supply was sitting on it(yeah that is right it was.).
You may with to try some tests in Windows to generate a load on the cpu like Prime 95 and the video card with something like furmarks(or just vary the video card fan speeds with MSI Afterburner. See if a sudden increase of lets say 5-10% makes a click or not).
If you can make the sound happen on command, you can get into the system and listen for it.
Coils can also make a noise, but it should be more of a oscillating buzzing type sound not a click.